March 2012 - galaxy-dev - lists.galaxyproject.org

Double setup
by Ian Porter (NBI) 05 Mar '12

05 Mar '12

Hi All, I was wondering if I could have some advice/ and if this is a workable solution. Basically there is a requirement to have both AD and Local accounts to be able to use galaxy on a VM. So I have setup apache to have the two URL's http://here.com/AD/ and http://here.com/Local/ to goto there relevant place with using the same galaxy backend files for both setups of galaxy but only having a different universe_wsgi.ini for the AD version and universe_local_wsgi.ini for the local, and the [filter:proxy-prefix] for both to have either AD or Local as there prefix filters. It appears to work in that you are able to login to both, but was wondering if anyone is able to stop a fatal flaw in this setup because I have just set it up and not really used it. Regards Ian

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problems with display at UCSC
by Hans-Rudolf Hotz 05 Mar '12

05 Mar '12

Hi everybody This is kind of an embarrassing question, but I am struggling to get the "display at UCSC" to work. Finally after several years, our sysadmin agreed to change the Apache configuration (which handles the authentication via LDAP) according to the configuration provided in the wiki: http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy So, I thought this was a piece of cake to make the "display at UCSC" work. I changed the following (in order to prevent broken links on our production server, I have currently restricted it to "mm7", which nobody is using in our institute): in "universe_wsgi.ini", I have: 'ucsc_display_sites = main' in "tool-data/shared/ucsc/ucsc_build_sites.txt", I have: 'main http://genome.ucsc.edu/cgi-bin/hgTracks? mm7' For history items with "format: bed, database: mm7" I get the link: "display at UCSC 'main'", eg: http://galaxy.fmi.ch/datasets/13185/display_at/ucsc_main?redirect_url=http%… If I click on it, I get the right UCSC page (ie: mm7 chr1:chr1:11,873-1,655,775). But I get the following error message on the top of the page: "Expected 200 http://galaxy.fmi.ch/root/display_as?id=13185&display_app=ucsc&authz_method…: 401 Authorization Required" Our sysadmin insists this is a Galaxy error (ie wrong configuration in the Galaxy code), but I ran out of ideas what else would need changing in Galaxy to make the display work. Is there anything else I need to adjust in addition to the two changes in "universe_wsgi.ini" and "ucsc_build_sites.txt"? Or is the error (as I suspect) somewhere in the Apache configuration. Thank you very much for any pointers which might get the display to work for us Regards, Hans

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Error running SICER
by Vidya .H.K 05 Mar '12

05 Mar '12

Hi, I am trying SICER peak calling tool. I am getting the following error" An error occurred running this job: /bin/sh: SICER-rb.sh: not found Traceback (most recent call last): File "/home/root12/galaxy-dist/tools/peak_calling/sicer_wrapper.py", line 156, in <module> if __name__=="__main__": __main__() File "/home/root12/galaxy-dist/tools/peak_calling/sic " SICER is working fine with the sample when executed on the terminal. I have installed SICER version-1.1 on ubuntu. Is galaxy compatible with SICER version-1.1? Can anybody help me resolve this problem. Regards Vidya

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Tool Shed Automatic Install Behind NGINX Proxy
by Zachary Charlop-Powers 02 Mar '12

02 Mar '12

Hello Galaxy Team/Users, Thanks again for your great work. A few months back I setup a local Galaxy server behind Nginx and everything worked great except for the browser-based automatic-install of tools from Galaxy-main. Using the web interface I would click on "Install to local Galaxy" and get the following error message: The resource could not be found. No route for /repository/Noneadmin_toolshed/install_repository At the time I had absolutely no idea where the problem came from and the very helpful dev team assisted me in tracking the issue to a problem with the proxy configuration, however I was never able to resolve the issue despite tinkering with the proxy configuration. Since I need the proxy (on a computer with other web-facing services) and since I could install tools using mercurial I didn't follow up the issue, however, automatic-install of tools would be great to have. A similar error is in the archives for someone using Apache (http://galaxy-development-list-archive.2308389.n4.nabble.com/Toolshed-not-a… ) and when I e-mailed the author he said he hadn't been able to resolve the issue and had simply worked around it as I had. As my Galaxy setup is very straightforward and follows the Galaxy Wiki instructions, I am thinking that others must have encountered this same problem, so here is my question: 1. For users who have installed Galaxy and use either the Apache or Nginx proxy configuration from the Wiki, have you gotten the browser-based Automatic Install of toolshed tools to work? 2. If so - could you share your proxy setup with me? best, zach cp Zach Charlop-Powers Post-Doctoral Fellow Laboratory of Genetically Encoded Small Molecules Rockefeller University zcharlop(a)rockefeller.edu

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Galaxy strips CSS from HTML files
by Cory Spencer 02 Mar '12

02 Mar '12

Hello all - One of the Galaxy tools I've been developing generates HTML output which I'd styled using a <style>...</style> tag in the HTML header. After updating to the latest Galaxy release earlier today, the <html>, <head>...</head>, <style> and <body> tags started to get stripped from the output, rendering previously CSS styled output rather unstylish. Delving into things, I noticed a change committed in December that sanitizes the output for HTML files via a call to "sanitize_html": https://bitbucket.org/galaxy/galaxy-central/changeset/35fee32991ce#chg-lib/… The added lines 381 -> 383 in the new file appear to be causing this new behaviour. Is there any option for making this optional? What was the rational behind stripping out these tags on outputted HTML files? Thanks for any help! Cory Spencer

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ID providers other than OpenID
by Nikolai Vazov 02 Mar '12

02 Mar '12

Hi, we work at the University of Oslo, USIT, The Research Computing Service group (Norway). We are preparing a bioinformatics portal using Galaxy and one of the requirements for the University of Oslo production is to implement an authentication called FEIDE. Feide is local (for Norway) IDp service based on saml2 which is yet different from OpenID. It supposes the existence of metadata files on the sp server side containing blocks with, e.g. (for idp) 'SingleSignOnService' => 'https://idp.feide.no/simplesaml/saml2/idp/SSOService.php', 'SingleLogoutService' => 'https://idp.feide.no/simplesaml/saml2/idp/SingleLogoutServiceiFrame.php', 'SingleLogoutServiceResponse' => 'https://idp.feide.no/simplesaml/saml2/idp/SingleLogoutServiceiFrameResponse…', 'certFingerprint' => 'cde69e332fa7dd0eaa99ee0ddf06916e8942ac53', 'hint.cidr' => '158.38.0.0/16' These blocks are read during the authentication process. Galaxy seems to be only supporting OpenID and new idp-s are added simply by adding a new url to OPENID_PROVIDER variable. Is there a solution if we have to communicate metadata between idp and sp? And ... is your egg "python_openid-2.2.5-py2.6.egg" using pysaml? Can it be rescrambled such that it can read some pysaml metadata files. Thank you in advance Nikolay Vazov -- Nikolay Vazov, PhD Research Computing Centre - http://hpc.uio.no USIT, University of Oslo

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GATK Depth of Coverage error
by Curt Palm 02 Mar '12

02 Mar '12

I am trying to run GATK's DepthOFCoverage using intervals and get the following error: failure preparing job Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 59, in run_job job_wrapper.prepare() File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 424, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 1827, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/home/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1330381526_3_23629.py", line 402, in respond NotFound: cannot find 'omit_interval_statistics' while searching for 'gatk_param_type.omit_interval_statistics' the parameters used are: Tool: Depth of Coverage Name: Depth of Coverage on data 35 and data 27 (per locus coverage) Created: Feb 27, 2012 Filesize: 0 bytes Dbkey: human_g1k_v37 Format: rtable Tool Version: None Tool Standard Output: stdout Tool Standard Error: stderr Input Parameter Value Conditional (reference_source) 0 BAM file 35: Table Recalibration on data 33, data 31, and data 27 (BAM) Using reference genome human_g1k_v37 RefSeq Rod No dataset Partition type for depth of coverage sample Output format rtable Conditional (gatk_param_type) 1 How strict should we be in validating the pedigree information STRICT Genomic intervals 27: 5um_amplicons_hg19.picard.list Interval set rule UNION Conditional (downsampling_type) 0 Type of BAQ calculation to apply in the engine OFF BAQ gap open penalty (Phred Scaled) 40.0 Use the original base quality scores from the OQ tag False Value to be used for all base quality scores, when some are missing -1 How strict should we be with validation STRICT Interval merging rule ALL Disable experimental low-memory sharding functionality. False Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run False Conditional (analysis_param_type) 0 I can run this analysis outside of Galaxy with the command: java -jar /opt/GenomeAnalysisTK/GenomeAnalysisTK.jar -T DepthOfCoverage -et NO_ET -R /home/galaxy/genome/human_g1k_v37/picard/human_g1k_v37.fasta --partitionType sample --out out.txt --outputFormat rtable -I bamfile.bam --intervals intervals_picardList.list I'd like to add the DepthOfCoverage to the end of a work flow and get per base coverage for a set of amplicon coordinates, so using an interval file is needed. any suggestions on what is wrong? ******************************************************* Curtis J. Palm cpalm(a)stanford.edu Stanford Genome Technology Center MC: 8307 office: 650-812-1994 *******************************************************

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Using complete workflow in another workflow
by thondeboer＠me.com 01 Mar '12

01 Mar '12

Hi, How far along are we about thinking about being able to re-use a complete workflow as a workflow step in another workflow? This would really allow us to modularize certain aspects of the analyses and would allow us to re-use a workflow in another. Barring that, a simple copy/paste from one workflow into another would also really help... Any plans in that direction? Thanks Thon

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Trackster traceback on C. Cerevisiae mapped data
by Oleksandr Moskalenko 01 Mar '12

01 Mar '12

Hello, I am getting consistent breakage for a C. Cerevisiae reference and mapped dataset when trying to visualize the mapped data in Trackster. I'm running the latest galaxy-dist and Trackster appears to be generally working since I added a couple of reference genomes and users were able to visualize their data. I just rebuilt all relevant references for the sacCer3 (dbkey) genome by concatenating the UCSC chromosome fasta files and building both 2bit file and the bowtie index from the resulting fasta file. The reference genome comes up in the Trackster as I can see the sequence. However, adding a track from the bowtie-mapped data freezes at the "building index" stage and selecting a chromosome in Trackster produces an immediate traceback. Logs are below. Thanks, Alex 10.25.137.177 - - [01/Mar/2012:12:56:50 -0400] "GET /tracks/converted_datasets_state?hda_ldda=hda&dataset_id=0f5bae0d7db33d73&chrom=chrIII HTTP/1.1" 500 - "http://galaxy.hpc.ufl.edu/tracks/browser?dataset_id=0f5bae0d7db33d73&id=9b0…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_3) AppleWebKit/535.11 (KHTML, like Gecko) Chrome/17.0.963.56 Safari/535.11"Error - <type 'exceptions.EOFError'>:URL: http://galaxy.hpc.ufl.edu/tracks/converted_datasets_state?hda_ldda=hda&data… '/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response)File '/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response)File '/galaxy/run/prod/lib/galaxy/web/framework/middleware/remoteuser.py', line 111 in __call__ return self.app( environ, start_response )File '/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response)File '/galaxy/run/prod/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs )File '/galaxy/run/prod/lib/galaxy/web/framework/__init__.py', line 67 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ) )File '/galaxy/run/prod/lib/galaxy/web/controllers/tracks.py', line 546 in converted_datasets_state if not indexer.has_data( chrom ):File '/galaxy/run/prod/lib/galaxy/visualization/tracks/data_providers.py', line 566 in has_data st = summary_tree_from_file( self.converted_dataset.file_name )File '/galaxy/run/prod/lib/galaxy/visualization/tracks/summary.py', line 92 in summary_tree_from_file return cPickle.load(open(filename, "rb"))EOFError: CGI Variables ------------- QUERY_STRING: 'hda_ldda=hda&dataset_id=0f5bae0d7db33d73&chrom=chrIII' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x6323cd0> paste.cookies: (<SimpleCookie: __utma='239163719.1605318534.1329425338.1330006360.1330438487.6' __utmc='239163719' __utmz='239163719.1329425338.1.1.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=(not%20provided)' auth_probe='1' auth_tkt='ZWE0ZmY3MjkxYjdhM2Y0NWRkMjVhNTVkZWUzODBhYzc0ZjRmODRlYm9tQGhwYy51ZmwuZWR1ITEwMDAsMTAwMyFtYWxleDpPbGVrc2FuZHIgTW9za2FsZW5rbw%3D%3D' galaxysession='86cf583f63ab6865e8a46aa482c17c1f6ea618d0f448986bf2fc440587db06af6b9d9ac4eccca0fe'>, 'galaxysession=86cf583f63ab6865e8a46aa482c17c1f6ea618d0f448986bf2fc440587db06af6b9d9ac4eccca0fe; auth_probe=1; __utma=239163719.1605318534.1329425338.1330006360.1330438487.6; __utmc=239163719; __utmz=239163719.1329425338.1.1.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=(not%20provided); auth_tkt=ZWE0ZmY3MjkxYjdhM2Y0NWRkMjVhNTVkZWUzODBhYzc0ZjRmODRlYm9tQGhwYy51ZmwuZWR1ITEwMDAsMTAwMyFtYWxleDpPbGVrc2FuZHIgTW9za2FsZW5rbw%3D%3D') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x631c890> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x1314b10> paste.parsed_querystring: ([('hda_ldda', 'hda'), ('dataset_id', '0f5bae0d7db33d73'), ('chrom', 'chrIII')], 'hda_ldda=hda&dataset_id=0f5bae0d7db33d73&chrom=chrIII') paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True webob._parsed_query_vars: (MultiDict([('hda_ldda', 'hda'), ('dataset_id', '0f5bae0d7db33d73'), ('chrom', 'chrIII')]), 'hda_ldda=hda&dataset_id=0f5bae0d7db33d73&chrom=chrIII') wsgi process: 'Multithreaded' ------------------------------------------------------------

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Error trying to enable samtools_mpileup
by Waldron, Michael H 01 Mar '12

01 Mar '12

I am running a local copy of Galaxy, last ran 'hg pull -u' on 2/20/12. I am trying to enable use of Mpileup for SAM Tools, and have added the entry for the samtools_mpileup.xml file in tool_conf.xml. However, when I startup Galaxy, the link for Mpileup does not appear in the Tools pane, and I see the following errors from the Galaxy startup: galaxy.tools ERROR 2012-02-29 16:28:51,919 error reading tool from path: samtools/samtools_mpileup.xml Traceback (most recent call last): File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 212, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 305, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 531, in __init__ self.parse( root, guid=guid ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 641, in parse self.parse_inputs( root ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 723, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 922, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 989, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 945, in parse_input_elem group.inputs = self.parse_input_elem( elem, enctypes, context ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 1015, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 1027, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 1330, in __init__ ToolParameter.__init__( self, tool, elem ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/data/__init__.py", line 21, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'sam_fa_indexes' Can someone tell me what is wrong here? Am I missing something in the database? Thanks, Mike Waldron

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